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173598 commits

Author SHA1 Message Date
Cayetano Santos
b8e2c8b3e1
gnu: Add emacs-pdd.
* gnu/packages/emacs-xyz.scm (emacs-pdd): New variable.

Change-Id: I605eb3a33746942e6defa92ff7c258faf9964581
Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com>
2025-11-07 18:39:28 +01:00
Cayetano Santos
7c5d3a11d2
gnu: emacs-bqn-mode: Update to 2025-07-06.
* gnu/packages/emacs-xyz.scm (emacs-bqn-mode): Update to 2025-07-06.

Change-Id: I6b2eae955fcb693564d82629a074b18f7bd48232
Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com>
2025-11-07 18:39:28 +01:00
Cayetano Santos
ea63507882
gnu: emacs-info-plus: Update to 0-5.a2322ad.
* gnu/packages/emacs-xyz.scm (emacs-info-plus): Update to 0-5.a2322ad.
[arguments]: Disable #:tests?.

Change-Id: I63ef215d9b3d66ace0393dbd9048422cedfd5260
Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com>
2025-11-07 18:39:28 +01:00
Cayetano Santos
611813d167
gnu: emacs-bitbake-modes: Update to 0.8.0.
* gnu/packages/emacs-xyz.scm (emacs-bitbake-modes): Update to 0.8.0.

Change-Id: I8fe6e9ee376d2751bfa1412a04a510b9556ebc33
Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com>
2025-11-07 18:39:28 +01:00
Cayetano Santos
0484a6ae9f
gnu: emacs-osm: Use new makeinfo phase.
* gnu/packages/emacs-xyz.scm (emacs-osm)[#:phases]<makeinfo>: Use
emacs-makeinfo.

Signed-off-by: Liliana Marie Prikler <liliana.prikler@gmail.com>
2025-11-07 18:39:27 +01:00
gemmaro
790a3936e4
gnu: uriparser: Update to 0.9.9.
* gnu/packages/web.scm (uriparser): Update to 0.9.9.

Change-Id: Ieb31a68806db14ffa9d42ea7cd0c897d08dab099
Signed-off-by: jgart <jgart@dismail.de>
2025-11-07 09:32:43 -06:00
Ricardo Wurmus
4bfe5cdf14
gnu: r-mzr: Skip two tests.
* gnu/packages/bioconductor.scm (r-mzr)[arguments]: Add phase 'skip-bad-tests.

Change-Id: I4395329993eeb76de9c820dcd5077f24acf53709
Signed-off-by: Simon Tournier <zimon.toutoune@gmail.com>
2025-11-07 13:54:47 +01:00
Sharlatan Hellseher
07a35c1790
gnu: Remove python-wget.
Project's source has gone
<https://bitbucket.org/techtonik/python-wget/>, PyPI shows that the
package was updated in 2015 <https://pypi.org/project/wget/#files>.

* gnu/packages/python-web.scm (python-wget): Delete variable.

Fixes: guix/guix#3321
Change-Id: I4d923baa67ebcfa3cc87620a98a0be30a9c429f7
2025-11-07 12:02:32 +00:00
Sharlatan Hellseher
536d3e6a04
gnu: Remove python-rawkit.
Fails to build, no users in Guix. The project never pass through alpha
stage.

Notes from upstream:

  rawkit is still alpha quality software. Until it hits 1.0, it may
  undergo substantial changes, including breaking API changes.

  This repository was archived by the owner on Oct 4, 2020. It is now
  read-only.

* gnu/packages/python-xyz.scm (python-rawkit): Delete variable.

Fixes: guix/guix#3265
Change-Id: I57950ba736e0b5de1e7a1bdf8cac65ec570cdb00
2025-11-07 12:02:32 +00:00
Sharlatan Hellseher
289390a0cd
gnu: Remove python-d2to1.
Fails to build, no longer required.

Note from upstream:

  This repository was archived by the owner on Jun 10, 2020. It is now
  read-only.

* gnu/packages/python-xyz.scm (python-d2to1): Delete variable.

Fixes: guix/guix#3251
Change-Id: I3c37e8f289026e1e8e5147a666f717c8310b5b9e
2025-11-07 12:02:32 +00:00
Sharlatan Hellseher
56282fa63f
gnu: Remove python-paste.
Fails to build, no users in Guix.

Note from upstream:

  Paste is in maintenance mode and recently moved from bitbucket to
  github. Patches are accepted to keep it on life support, but for the
  most part, please consider using other options.

Fixes: guix/guix#3229
* gnu/packages/python-web.scm (python-paste): Delete variable.

Change-Id: If4ee8da2a0c49f40676e32a934a6cfff81f3522d
2025-11-07 12:02:31 +00:00
Sharlatan Hellseher
7194e0379a
gnu: Remove python-pastescript.
It fails to build, no users in Guix.

Note from upstream:

  Paste Script is being maintained on life support. That means that
  critical bugs will be fixed, and support for new versions of Python
  will be handled, but other than that new features are not being
  considered.

* gnu/packages/python-web.scm (python-pastescript): Delete variable.

Change-Id: I399dcebd3a4329ed80d0eb0d3a2df01266272701
2025-11-07 12:02:31 +00:00
Sharlatan Hellseher
bf745a458d
gnu: Remove python-pyportmidi.
This package was required only to build frescobaldi which no longer
needs it, there are no other users in Guix, and it fails to build, see
<https://codeberg.org/guix/guix/pulls/3191>.

* gnu/packages/music.scm (python-pyportmidi): Delete variable.

Fixes: guix/guix#3202
Change-Id: I2cfff4416dfa0206d8b91b2d6682a2e2dba8ee48
2025-11-07 12:02:31 +00:00
Ricardo Wurmus
497dcabce7
gnu: r-voltron: Update to 0.2.1-1.1c0810b.
* gnu/packages/bioinformatics.scm (r-voltron): Update to 0.2.1-1.1c0810b.
[propagated-inputs]: Add r-biocsingular.

Change-Id: I3ae6971b14ceff7f6e367a3d0ca7dbaff00049ae
2025-11-07 12:33:44 +01:00
Simon Tournier
9567e23ad0
gnu: r-greylistchip: Fix tests.
* gnu/packages/bioconductor.scm (r-greylistchip)[native-inputs]: Add
r-biocstyle.

Change-Id: I0804d217c7005cdbcd3b344c5cbdc22eec14ddac
2025-11-07 11:17:17 +01:00
Simon Tournier
76d78fb106
gnu: r-colorout: Adjust GCC@14.
* gnu/packages/cran.scm (r-colorout)[arguments]: New phase that set GCC
compiler flag.

Change-Id: I7616cbd7918e00faed307dcc41dd6fe9cbc02086
2025-11-07 11:17:17 +01:00
Simon Tournier
5b07e039d1
gnu: r-gofuncr: Fix tests.
* gnu/packages/bioconductor.scm (r-gofuncr)[native-inputs]: Add
r-homo-sapiens.

Change-Id: I5c2759b73e98aa67136093c64d77be0a8e21e52d
2025-11-07 11:17:17 +01:00
Simon Tournier
10272557b7
gnu: r-blavaan: Adjust GCC@14.
* gnu/packages/cran.scm (r-blavaan)[arguments]: Add phase that decreases
GCC@14 strictness.

Change-Id: Ic56b3d6ba1b92ee98b57ebfe0db4c1aa2a542b24
2025-11-07 11:17:16 +01:00
Simon Tournier
fee483e713
gnu: r-densestbayes: Adjust GCC@14.
* gnu/packages/cran.scm (r-densestbayes)[arguments]: Add phase that decreases
GCC@14 strictness.

Change-Id: I52c45b9f693d843f25f1d61ef440e5b1cf2808d2
2025-11-07 11:17:16 +01:00
Simon Tournier
594f1a55bf
gnu: r-dada2: Adjust GCC@14.
* gnu/packages/bioconductor.scm (r-dada2)[arguments]: Add phase that decreases
GCC@14 strictness.

Change-Id: Ie488f6f2ecffa38b1327ec5efb726c49c2c04319
2025-11-07 11:17:15 +01:00
Simon Tournier
5797a07454
gnu: r-dtwclust: Adjust GCC@14.
* gnu/packages/cran.scm (r-dtwclust)[arguments]: Add phase that decreases
GCC@14 strictness.

Change-Id: I4235fb9444e67112ee0906b479445b5b1c5ef7b0
2025-11-07 11:17:15 +01:00
Ricardo Wurmus
93d892f333
gnu: r-rffc: Adjust to R@4.5.0.
* gnu/packages/cran.scm (r-rffc)[arguments]: Replace Calloc and Free by
R_Calloc and R_Free.

Change-Id: I5102fff078f8ca2440dae250b9d439e5440fe394
Signed-off-by: Simon Tournier <zimon.toutoune@gmail.com>
2025-11-07 11:17:10 +01:00
Ricardo Wurmus
3945e556c7
gnu: r-rcppparallel: Patch TBB task.h.
Patching this file lets us compile downstream packages without errors.

* gnu/packages/cran.scm (r-rcppparallel)[arguments]: Add phase 'gcc-compatibility.

Change-Id: I966c09887f1536dcc623d322f6b141fad069e3dd
Signed-off-by: Simon Tournier <zimon.toutoune@gmail.com>
2025-11-07 11:17:01 +01:00
Simon Tournier
80804e10c8
gnu: r-rstan: Adjust GCC@14.
* gnu/packages/bioconductor.scm (r-rstan)[arguments]: Add phase that decreases
GCC@14 strictness.

Change-Id: I83920c1acfd944f36625385012f0dd28bbc3decc
2025-11-07 09:55:48 +01:00
Simon Tournier
8c4c02db2a
gnu: r-chromstar: Adjust R@4.5.0 and GCC@14.
* gnu/packages/bioinformatics.scm (r-chromstar)[arguments]: Add phase that
replaces C-level facilities from R@4.5.0.

Change-Id: I16deb4b68beaf5665d57bd2045dc91a043c46e82
2025-11-07 09:55:48 +01:00
Simon Tournier
6ea5c58a1f
gnu: r-chipkernels: Adjust R@4.5.0 and GCC@14.
* gnu/packages/bioinformatics.scm (r-chipkernels)[arguments]: Add phase that
replaces C-level facilities from R@4.5.0.

Change-Id: Iac58b4d871160b4cbfd8b71d771c2f2fcf174240
2025-11-07 09:55:47 +01:00
Simon Tournier
2fef4214ad
gnu: Remove r-assertive-reflection.
Package was removed from the CRAN repository and it depends on `'is.R()`
removed by R@4.5.0.

* gnu/packages/cran.scm (r-assertive-reflection): Delete variable.

Change-Id: I373b23e0a450c096799199d719d23dea11f5f9f3
2025-11-07 09:55:47 +01:00
Simon Tournier
6c20f0eeb1
gnu: Remove r-assertive.
Package was removed from the CRAN repository and its dependency
'r-assertive-reflection' relies on the R procedure 'is.R()' which had been
removed in R@4.5.0.

* gnu/packages/cran.scm (r-assertive): Delete variable.

Change-Id: I1a8126594162b0c0f4ef03a9177fb5b74c4754be
2025-11-07 09:55:47 +01:00
Simon Tournier
9e6abc08ed
gnu: r-aneufinder: Adjust R@4.5.0 and GCC@14.
* gnu/packages/bioconductor.scm (r-aneufinder)[arguments]: Add phases that
relax GCC@14 strictness when using R@4.5.0 C-level facilities.

Change-Id: If524806121e7b6f697b0cdee75cbe1aef3bb7b9a
2025-11-07 09:55:46 +01:00
Simon Tournier
c050da2303
gnu: r-paralleldist: Adjust GCC@14.
* gnu/packages/cran.scm (r-paralleldist)[arguments]: Add phase that relax
GCC@14 strictness.

Change-Id: I7dd04d8547b35cb35fac0d1386185d37239d4a8e
2025-11-07 09:55:46 +01:00
Simon Tournier
70c7c39170
gnu: r-cner: Adjust GCC@14.
* gnu/packages/bioconductor.scm (r-cner)[arguments]: Add phase that decreases
GCC@14 strictness.

Change-Id: I25a05c9946305fec133a244f310b0fb949dc67d1
2025-11-07 09:55:46 +01:00
Simon Tournier
944271100d
gnu: r-simpleaffy: Adjust GCC@14.
* gnu/packages/bioconductor.scm (r-simpleaffy)[arguments]: Add phases that
turns compilation error into warning.

Change-Id: Id73f60872d72c018074a5cd019953bdb2ed6694b
2025-11-07 09:55:45 +01:00
Simon Tournier
21065459b1
gnu: r-ifultools: Adjust R@4.5.0 and GCC@14.
* gnu/packages/cran.scm (r-ifultools)[]arguments]: Add phase which adjust
C-level facilities Calloc, Free and Realloc.

Change-Id: I0414a805af1550be738b2ce0259318dbf3aecf15
2025-11-07 09:55:45 +01:00
Simon Tournier
62bfec2a8d
gnu: r-decon: Adjust to R@4.5.0 and GCC@14.
* gnu/packages/cran.scm (r-decon)[arguments]: Add phase which replaces C-level
PI by M_PI.

Change-Id: I68a5f3ce808761880b6ff7780b2e1781d7164038
2025-11-07 09:55:44 +01:00
Simon Tournier
4e1e433cdf
gnu: r-rserve: Adjust R@4.5.0 and GCC@14.
* gnu/packages/cran.scm (r-rserve)[arguments]: Adjust compiler flags.

Change-Id: Ic3125adb771fda68a7a0e70c8a6c0c72ff14e3e2
2025-11-07 09:55:44 +01:00
Simon Tournier
7c6e8e7d8d
gnu: r-rbamtools: Adjust R@4.5.0 and GCC@14.
* gnu/packages/cran.scm (r-rbamtools)[arguments]: Replace C-level procedures
Calloc and Free by R_Calloc and R_Free.

Change-Id: I8611f800ad291c764fa295da7b00083d2bb40e95
2025-11-07 09:55:44 +01:00
Simon Tournier
b09f4fbaf7
gnu: r-harshlight: Adjust to GCC@14.
* gnu/packages/bioconductor.scm (r-harshlight)[arguments]: Add phases that
passes CFLAGS.

Change-Id: I54263d82d9fb97253bdbebc2f070d3da7325b163
2025-11-07 09:55:43 +01:00
Simon Tournier
50b254f2fe
gnu: r-ibdreg: Adjust to R@4.5.0 and GCC@14.
* gnu/packages/cran.scm (r-ibdreg)[arguments]: Replace Calloc and Free by
R_Calloc and R_Free.

Change-Id: I4022505ea4be164588c58f27561fc13d286545e8
2025-11-07 09:55:43 +01:00
Simon Tournier
183bf941c5
gnu: r-rbowtie: Reset zlib as inputs.
Follow up of c0709a05ab.

* gnu/packages/bioconductor.scm(r-rbowtie)[inputs]: Add zlib.

Change-Id: I9a7b09e50c7a2d25304925ee05cfce28b6c5e8c8
2025-11-07 09:55:43 +01:00
Simon Tournier
da9a52da9f
gnu: r-freetypeharfbuzz: Adjust configure flags for meson-build-system.
Follow up of 5a361d46ba.

* gnu/packages/cran.scm (r-freetypeharfbuzz): Remove 'static-package' package
procedure.
[arguments]<configure-flags>: Adapt flags for meson-build-system.

Change-Id: Ia24aac55378c697a4a0c34e989680457e8e22347
2025-11-07 09:55:42 +01:00
Simon Tournier
a54614f688
gnu: r-ihw: Missing dependencies for tests.
* gnu/packages/bioconductor.scm (r-ihw)[native-inputs]: Add r-ggplot2 and
r-scales.

Change-Id: I9777c90bb62ec614daa469941f8db69b0357e961
2025-11-07 09:55:42 +01:00
Simon Tournier
1ed95fb01a
teams: r: Add manifest.
* etc/teams/r/r-manifest.scm: New file.

Change-Id: I8191136b81a762bdb219fe45dcd6dd022b8cf758
2025-11-07 09:55:41 +01:00
Hartmut Goebel
3b88fe6200
gnu: Add python-dependency-groups.
* gnu/packages/python-web.scm (python-dependency-groups): New variable.

Change-Id: I1b284453f9ee0602e71dbfc8c6742cd3802c30f6
2025-11-07 00:35:27 +01:00
Yelninei
04ad78093a
gnu: grep: Don't override XFAIL_TESTS on 32bit Hurd.
Some tests in grep are marked as XFAIL.
Setting XFAIL_TESTS will cause these to fail.

Fixes guix/guix#4083.

* gnu/packages/base.scm (grep)[arguments]: Move skipping of test-year2038 on
32bit hurd from make-flags to a phase.

Change-Id: I4e42fe64f7ff8213bf43147c9e444891d3bedb91
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2025-11-06 23:29:46 +01:00
Zhu Zihao
5e111f9999
gnu: chez-irregex: Update to 0.9.11.
* gnu/packages/patches/chez-irregex-import-cond-expand.patch: New file.
* gnu/local.mk (dist_patch_DATA): New entry for
chez-irregex-import-cond-expand.patch.
* gnu/packages/chez.scm (chez-irregex): Update to 0.9.11.
[source]: Switch to the original upstream and apply the patch.
[arguments]<#:test-target><#:tests?>: Disable test since it's not available in
Chez.
<#:phases>:
In phase 'configure', setup CHEZSCHEMELIBDIRS environment variable.
In phase 'build', run 'make chez-build'.
In phase 'install', run 'make chez-install'.
[home-page]: Switch to the original homepage.

Change-Id: I1da16657cc41d278803c20ef7d674a8fdc928c00
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2025-11-06 23:29:46 +01:00
Sören Tempel
08db14c74f
file-systems: Support the 'remount' mount flag.
This allows remounting file systems which are already mounted by
the initrd with custom mount options (e.g. /proc with hidepid=2).

* gnu/build/file-systems.scm (mount-flags->bit-mask): Map 'remount
to MS_REMOUNT.
* gnu/system/file-systems.scm (invalid-file-system-flags): Add
'remount to the list of KNOWN-FLAGS.
* doc/guix.texi (File Systems): Document it.

Fixes: guix/guix#3849
Change-Id: I0ab116a5b4f7bd201e955ecf022e260c63828dc4
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2025-11-06 23:29:46 +01:00
Kjartan Oli Agustsson
b2a6f65753
doc: Fix documentation of unattended-upgrade-service
* doc/guix.texi (Unattended Upgrades): Replace mention of mcron with Shepherd
Timers.

Change-Id: I7e0a509a33e15834429ec4cc0b735a5247cff9d9
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2025-11-06 23:29:45 +01:00
Charles Roelli
189712d428
gnu: python-django-4: Update to 4.2.26.
* gnu/packages/django.scm (python-django-4): Update to version 4.2.26.

Change-Id: I06278a655b3fa95883944ea374d8e16b9065f1ea
Signed-off-by: jgart <jgart@dismail.de>
2025-11-06 12:57:24 -06:00
Charles Roelli
c1f4c8b42b
gnu: python-django: Update to 5.2.8.
* gnu/packages/django.scm (python-django): Update to version 5.2.8.

Change-Id: I1827f8d0174da853069e716bfe5199679aaca33e
Signed-off-by: jgart <jgart@dismail.de>
2025-11-06 12:57:15 -06:00
Brendan Tildesley
17da19f4bc
gnu: ccfits: fix source url
* gnu/packages/astronomy.scm (ccfits): Fix source url.

Change-Id: Ib9779cb6cf97972fae668a430bc3156ab89e3e6b
Modified-by: Sharlatan Hellseher <sharlatanus@gmail.com>
Signed-off-by: Sharlatan Hellseher <sharlatanus@gmail.com>
2025-11-06 16:05:37 +00:00